Organism : Bacillus cereus ATCC14579 | Module List:
Module 322 Profile

GeneModule member RegulatorRegulator MotifMotif
Network Help

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges.

Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif
Regulators for Module 322

There are 10 regulatory influences for Module 322

Regulator Table (10)
Regulator Name Type
BC2434 tf
BC0648 tf
BC3449 tf
BC0116 tf
BC4703 tf
BC3922 tf
BC4499 tf
BC4652 tf
BC0954 tf
BC0598 tf

Regulator Help

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type.

tf: Transcription factor

ef: Environmental factor

combiner: Combinatorial influence of a tf or an ef through logic gate. Table is sortable by clicking on the arrows next to column headers.

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
4558 3.60e-06 AGGGGG
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4559 1.00e+03 gatgcg.aAaaTgCt.TcT
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment

Regulon 322 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 0.00e+00 1.00e-06 15/23
Carbohydrate Metabolism kegg subcategory 0.00e+00 0.00e+00 9/23
Citrate cycle (TCA cycle) kegg pathway 0.00e+00 0.00e+00 8/23
Butanoate metabolism kegg pathway 1.00e-05 2.17e-04 3/23
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 9/23
Oxidative phosphorylation kegg pathway 5.60e-05 7.83e-04 3/23
Carbon fixation pathways in prokaryotes kegg pathway 0.00e+00 0.00e+00 7/23
Glycine serine and threonine metabolism kegg pathway 1.30e-05 2.62e-04 3/23
Global kegg category 0.00e+00 1.00e-06 14/23
Metabolism kegg subcategory 0.00e+00 1.00e-06 14/23
Metabolic pathways kegg pathway 0.00e+00 0.00e+00 14/23
Biosynthesis of secondary metabolites kegg pathway 0.00e+00 8.00e-06 9/23
Microbial metabolism in diverse environments kegg pathway 0.00e+00 0.00e+00 9/23

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 0.00e+00 0.00e+00 8/23
TCA cycle tigr sub1role 0.00e+00 0.00e+00 7/23

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 9.00e-06 3.70e-05 15/23
Signal transduction mechanisms cog subcategory 7.29e-03 1.27e-02 3/23
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 8/23
Amino acid transport and metabolism cog subcategory 1.75e-02 2.90e-02 4/23
Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 cog 0.00e+00 0.00e+00 3/23
Functions Help

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Members for Module 322

There are 23 genes in Module 322

Gene Member Table (23)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0442 BC0442 CDS None chromosome 430766 431362 + Tellurium resistance protein terD (NCBI ptt file) False
BC0443 BC0443 CDS None chromosome 431379 431969 + Tellurium resistance protein terD (NCBI ptt file) False
BC0444 BC0444 CDS None chromosome 432055 432633 + Tellurium resistance protein terD (NCBI ptt file) False
BC1224 BC1224 CDS None chromosome 1201487 1201909 - Acetyltransferase (NCBI ptt file) False
BC1225 BC1225 CDS None chromosome 1201911 1202429 - 2'-5' RNA ligase (NCBI ptt file) False
BC2101 BC2101 CDS None chromosome 2043162 2044850 + Formate--tetrahydrofolate ligase (NCBI ptt file) False
BC2434 BC2434 CDS None chromosome 2377436 2377918 + Transcriptional regulator, MarR family (NCBI ptt file) True
BC2435 BC2435 CDS None chromosome 2378085 2378822 + Phosphoglycerate mutase (NCBI ptt file) False
BC2436 BC2436 CDS None chromosome 2379061 2379798 + SpoIISA like protein (NCBI ptt file) False
BC3833 BC3833 CDS None chromosome 3812313 3813215 - Succinyl-CoA synthetase alpha chain (NCBI ptt file) False
BC3834 BC3834 CDS None chromosome 3813235 3814395 - Succinyl-CoA synthetase beta chain (NCBI ptt file) False
BC4224 BC4224 CDS None chromosome 4173332 4174936 - Glycine dehydrogenase [decarboxylating] (NCBI ptt file) False
BC4225 BC4225 CDS None chromosome 4174933 4176276 - Glycine dehydrogenase [decarboxylating] (NCBI ptt file) False
BC4226 BC4226 CDS None chromosome 4176297 4177397 - Aminomethyltransferase (NCBI ptt file) False
BC4516 BC4516 CDS None chromosome 4460223 4460984 - Succinate dehydrogenase iron-sulfur protein (NCBI ptt file) False
BC4517 BC4517 CDS None chromosome 4460977 4462770 - Succinate dehydrogenase flavoprotein subunit (NCBI ptt file) False
BC4518 BC4518 CDS None chromosome 4462784 4463410 - Succinate dehydrogenase cytochrome b558 subunit (NCBI ptt file) False
BC4571 BC4571 CDS None chromosome 4516713 4517804 - Deblocking aminopeptidase (NCBI ptt file) False
BC4592 BC4592 CDS None chromosome 4538061 4538999 - Malate dehydrogenase (NCBI ptt file) False
BC4593 BC4593 CDS None chromosome 4539019 4540311 - Isocitrate dehydrogenase [NADP] (NCBI ptt file) False
BC4594 BC4594 CDS None chromosome 4540472 4541587 - Citrate synthase (NCBI ptt file) False
BC4921 BC4921 CDS None chromosome 4831788 4833272 - Cytosol aminopeptidase (NCBI ptt file) False
BC4926 BC4926 CDS None chromosome 4836736 4837731 + Thioredoxin reductase (NCBI ptt file) False

Genes Help

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Module Overview

The landing module page shows quick summary info including co-expression profiles, de-novo identified motifs, and transcription factors and/or environmental factors as regulatory influences. It also includes module residual, motif e-values, conditions and links to other resources such as NCBI and Microbesonline. . If a transcription factor is included in the manually curated RegPrecise database, further information from RegPrecise is shown, allowing users to perform comparative analysis.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Network

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges. Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Functions

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Genes

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Social

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Definitions

Residual: is a measure of bicluster quality. Mean bicluster residual is smaller when the expression profile of the genes in the module is "tighter". So smaller residuals are usually indicative of better bicluster quality.

Expression Profile: is a preview of the expression profiles of all the genes under subset of conditions included in the module. Tighter expression profiles are usually indicative of better bicluster quality.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Genes: Number of genes included in the module.

Functions: We identify functional enrichment of each module by camparing to different functional categories such as KEGG, COG, GO etc. by using hypergeometric function. If the module is significantly enriched for any of the functions, this column will list few of the these functions as an overview. Full list of functions is available upon visiting the module page under the Functions tab.